Contacts of the strand formed by residues 46 - 50 (chain A) in PDB entry 2LDX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 3.0 45.0 + - + +
22A ILE 2.9 23.2 + - - -
44A ALA* 3.3 4.4 - - - +
45A ASP* 1.3 82.9 + - - +
47A LEU* 1.3 63.1 - - - +
75A LYS* 2.5 64.8 + - + +
77A VAL* 2.9 26.1 - - + +
84A VAL 4.9 0.3 - - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 3.0 22.0 - - + +
24A VAL* 5.0 6.3 - - + -
35A ALA* 4.6 9.2 - - + +
38A ILE* 3.4 35.2 - - + -
39A LEU* 4.3 20.6 - - + -
44A ALA* 4.6 4.7 - - + +
46A GLU* 1.3 76.8 - - - +
48A ALA* 1.3 60.6 + - - +
49A LEU* 3.6 28.9 - - + -
64A LEU* 5.1 2.5 - - + -
73A THR* 4.9 6.5 - - - +
75A LYS 3.2 7.5 + - - +
76A ILE* 3.3 16.9 - - + +
77A VAL 3.1 20.5 + - - +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 3.8 9.4 - - - -
22A ILE 2.9 5.1 + - - -
23A THR* 2.9 42.6 - - + +
24A VAL 3.0 2.9 + - - -
46A GLU 4.1 0.8 - - - -
47A LEU* 1.3 73.8 - - - +
49A LEU* 1.3 63.9 + - - +
50A VAL* 4.0 0.9 - - + -
77A VAL* 3.2 23.3 - - + +
84A VAL* 3.3 27.4 - - + +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.6 14.4 - - + +
27A VAL* 4.5 18.2 - - + -
32A MET* 5.1 2.9 - - + -
35A ALA* 5.1 6.5 - - + -
47A LEU* 3.6 26.0 - - + +
48A ALA* 1.3 74.9 - - - +
50A VAL* 1.3 61.6 + - - +
51A ASP 4.0 0.2 - - - -
57A LEU* 3.4 30.5 - - + +
61A ALA* 3.4 15.0 - - + -
64A LEU* 4.1 21.8 - - + -
76A ILE* 4.7 6.3 - - + -
77A VAL 2.7 28.1 + - - +
78A PHE* 2.9 40.1 - - + +
79A GLY 3.4 2.8 + - - -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A THR* 4.2 15.7 - - + -
24A VAL 3.1 7.5 + - - -
25A VAL* 3.1 17.1 - - + +
26A GLY 2.6 29.1 + - - -
48A ALA 4.0 0.6 + - - -
49A LEU* 1.3 74.8 - - - +
51A ASP* 1.3 59.9 + - - +
79A GLY 3.5 9.4 - - - +
80A LYS 4.8 0.7 - - - -
81A ASP 3.8 26.7 - - - +
82A TYR* 3.5 41.7 - - + +
84A VAL* 4.5 16.4 - - + +
85A SER* 4.6 6.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il